Full ribosomal operon sequencing of anaerobic gut fungi (phylum Neocallimastigomycota): insights on its markers and phylogenetic resolution
Year: 2026
Type: article
Abstract: The phylogenetic affiliations of anaerobic gut fungi ( Neocallimastigomycota ) are typically evaluated using single-gene markers. However, this approach often fails to resolve relationships between closely related lineages. To address this issue and identify alternative markers, we created a curated database comprising the complete ribosomal operon sequences of 156 isolates, representing 20 of the 22 recognized genera and two new genus-level clades. Using long-read sequencing, we obtained ~9 kbp operon sequences and developed a robust analysis pipeline. Incorporating both coding genes and non-coding regions (excluding IGS1) improved phylogenetic resolution. This phylogenetic approach successfully resolved the Cyllamyces and Caecomyces clades (hard-to-distinguish genetically), as well as seven analysed Piromyces species. We also scanned the operon for markers that are suitable for short-read sequencing platforms, with the aim of enhancing biodiversity and phylogenetic studies. Notably, the ETS1 genetic region also enabled the distinction between these lineages, indicating its phylogenetic value within the ribosomal operon. The resulting database is a valuable resource for expanding and strengthening phylogenetic frameworks.
Source: IMA Fungus
Authors: Diana Young, Katrin Stüer-Patowsky, Liren Huang, Mostafa S. Elshahed, Noha H. Youssef, Radwa Hanafy, Yanfen Cheng, Christina D. Moon, Priya Soni, Akshay Joshi, Marcus Stabel, Katrin Ochsenreither, Sumit Singh Dagar, Ethan Hillman, Kevin V. Solomon, Katerina O. Fliegerová, Gareth W. Griffith, Tony M. Callaghan, Sabine M. Podmirseg, Alexander Sczyrba, Veronika Flad, Michael Lebuhn, Christian Wurzbacher
Institutions: Bavarian State Research Center for Agriculture, Technical University of Munich, Bielefeld University, Oklahoma State University, Nanjing Agricultural University, AgResearch, Bioeconomy Science Institute, ZHAW Zurich University of Applied Sciences, Karlsruhe Institute of Technology, University of Applied Sciences Kaiserslautern, Agharkar Research Institute, University of Michigan, University of Delaware, Czech Academy of Sciences, Czech Academy of Sciences, Institute of Animal Physiology and Genetics, Aberystwyth University, Universität Innsbruck, Forschungszentrum Jülich
Language: English
Subfield: Plant Science
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,490
Funders: National Science Foundation, U.S. Department of Energy, Arthritis National Research Foundation, Purdue University, AgResearch, National Research Foundation, Department of Science and Technology, Ministry of Science and Technology, India, Deutsche Forschungsgemeinschaft, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, National Natural Science Foundation of China, Austrian Science Fund, Ministry of Business, Innovation and Employment, Nanjing Agricultural University, Universität Innsbruck, National Institutes of Health, Office of Science, Agharkar Research Institute, Biological and Environmental Research
Awards: Unleashing the hidden potential of the anaerobic fungi, G1993999166, GENETIC TOOLS TO OPTIMIZE LIGNOCELLULOSE CONVERSION IN
ANAEROBIC FUNGI AND INTERROGATE THEIR GENOMES, G3267677622, G3476975150, PurSUit: Discovery, characterization, and elucidation of the global patterns and determinants of anaerobic fungal (Neocallimastigomycota) diversity in the herbivorous gut, G3759436777, G4213440006, G4400276964, G5256267526, SSIF Programmes AgResearch, G5448623231, G5587260680, G8293225600, G8590477180, G8809671385, G9000352532
OpenAlex ID: W7204255692